d-seams / pyseams

python bindings to seams-core

pyseams

Python bindings to the C++ engine (seams-core) of the d-SEAMS (Deferred Structural Elucidation Analysis for Molecular Simulations) project.

Contributions

All contributions are welcome, this includes code and documentation contributions but also questions or other clarifications. Note that we expect all contributors to follow our Code of Conduct.

Acknowledgments

This project was conceived as part of d-SEAM’s participation under the Python Software Foundation (PSF) in the 2023 iteration of the Google Summer of Code programme.

License

MIT.

pyseams's Issues

chillPlus analysis failing

similar to the bulkTopologicalCriterion analysis failure, this chillPlus analysis is also failing

The input iceNeighbourList is defined as std::vectorstd::vector iceList in main.cpp file is compiling but throwing a runtime error.

Refer the commit for the chillPlus.py file.

here are the steps to recreate the error.

gh repo clone d-SEAMS/pyseams
micromamba env create -f environment.yml
micromamba activate pyseamsdev
mkdir bbdir
cd bbdir
meson setup bbdir
meson compile -C bbdir
meson install -C bbdir
cd ../
python chillPlus.py

BUG: Hardcoded paths in some files

pyseams/pyb11_srcs/py_one.cc

Lines 7 to 14 in aa099de

	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/neighbours.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/bond.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/franzblau.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/ring.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/topo_one_dim.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/bulkTUM.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/selection.hpp"
	#include "/users/home/ruhila/Git/Github/dSEAMS/pyseams/subprojects/seams-core/src/include/internal/topo_two_dim.hpp"

These will make it very unlikely to compile on another machine, @RuhiRG.

bulkTopologicalCriterion analysis failing

The input iceNeighbourList is defined as std::vector<std::vector> iceList in main.cpp file is compiling but throwing a runtime error.

Refer the commit 817b2ca for the bulktopoC.py file.

here are the steps to recreate the error.

gh repo clone d-SEAMS/pyseams
micromamba env create -f environment.yml
micromamba activate pyseamsdev
mkdir bbdir
cd bbdir
meson setup bbdir
meson compile -C bbdir
meson install -C bbdir
cd ../
python bulktopoC.py

CI: Needs Github Actions

It would be nice to have some automated tests. For starters perhaps just to close this issue, a build test on ubuntu-latest would be good.

This is very basic but shows the basic layout:

name: Build and Test
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  buildmamba:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
        with:
          submodules: "recursive"
          fetch-depth: 0
      - name: Install Conda environment
        uses: mamba-org/provision-with-micromamba@main
      - name: Build
        shell: bash -l {0}
        run: |
          meson setup bbdir
          meson compile -C bbdir

Perhaps also a test stage for now. The official GHA documentation has a lot of advice. Also it is always a good idea to check the workflows used in other projects :)